-
"X":
-
fixed-effects model matrix
-
"Z":
-
random-effects model matrix
-
"Zt":
-
transpose
of random-effects model matrix. Note that the structure
of Zt has changed since lme4.0; to get a
backward-compatible structure, use
do.call(Matrix::rBind,getME(.,"Ztlist"))
-
"Ztlist":
-
list of components of the transpose of the
random-effects model matrix, separated by individual
variance component
-
"mmList":
-
list of raw model matrices associated with random
effects terms
-
"y":
-
response vector
-
"mu":
-
conditional mean of the response
-
"u":
-
conditional mode of the “spherical”
random effects variable
-
"b":
-
conditional mode of the
random effects variable
-
"Gp":
-
groups pointer vector.
A pointer to the beginning of each group of random
effects corresponding to the random-effects terms,
beginning with 0 and including a final element giving the
total number of random effects
-
"Tp":
-
theta pointer vector. A pointer to the beginning of the theta
sub-vectors corresponding to the random-effects terms,
beginning with 0 and including a final element giving the
number of thetas.
-
"L":
-
sparse Cholesky factor of the penalized random-effects model.
-
"Lambda":
-
relative covariance factor Lambda of the random effects.
-
"Lambdat":
-
transpose Lambda' of Lambda above.
-
"Lind":
-
index vector for inserting elements of
theta into the nonzeros of Lambda.
-
"Tlist":
-
vector of template matrices from which the blocks of
Lambda are generated.
-
"A":
-
Scaled sparse model matrix (class
"dgCMatrix") for
the unit, orthogonal random effects, U, equal to
getME(.,"Zt") %*% getME(.,"Lambdat")
-
"RX":
-
Cholesky factor for the fixed-effects parameters
-
"RZX":
-
cross-term in the full Cholesky factor
-
"sigma":
-
residual standard error; note that sigma(object) is preferred.
-
"flist":
-
a list of the grouping variables (factors)
involved in the random effect terms
-
"fixef":
-
fixed-effects parameter estimates
-
"beta":
-
fixed-effects parameter estimates (identical
to the result of fixef, but without names)
-
"theta":
-
random-effects parameter estimates: these
are parameterized as the relative Cholesky factors of
each random effect term
-
"ST":
-
A list of S and T factors in the TSST' Cholesky
factorization of the relative variance matrices of the random
effects associated with each random-effects term. The unit lower
triangular matrix, T, and the diagonal matrix, S, for
each term are stored as a single matrix with diagonal elements
from S and off-diagonal elements from T.
-
"n_rtrms":
-
number of random-effects terms
-
"n_rfacs":
-
number of distinct random-effects grouping factors
-
"N":
-
number of rows of X
-
"n":
-
length of the response vector, y
-
"p":
-
number of columns of the fixed effects model matrix, X
-
"q":
-
number of columns of the random effects model matrix, Z
-
"p_i":
-
numbers of columns of the raw model matrices, mmList
-
"l_i":
-
numbers of levels of the grouping factors
-
"q_i":
-
numbers of columns of the term-wise model matrices, ZtList
-
"k":
-
number of random effects terms
-
"m_i":
-
numbers of covariance parameters in each term
-
"m":
-
total number of covariance parameters, i.e., the
same as dims@nth below.
-
"cnms":
-
the “component names”, a list.
-
"REML":
-
0 indicates the model was fitted by maximum
likelihood, any other positive integer indicates fitting by
restricted maximum likelihood
-
"is_REML":
-
same as the result of isREML(.)
-
"devcomp":
-
a list consisting of a named numeric vector,
cmp, and a named integer vector, dims, describing
the fitted model. The elements of cmp are:
- ldL2
-
twice the log determinant of L
- ldRX2
-
twice the log determinant of RX
- wrss
-
weighted residual sum of squares
- ussq
-
squared length of u
- pwrss
-
penalized weighted residual sum of squares,
“wrss + ussq”
- drsum
-
sum of residual deviance (GLMMs only)
- REML
-
REML criterion at optimum (LMMs fit
by REML only)
- dev
-
deviance criterion at optimum
(models fit by ML only)
- sigmaML
-
ML estimate of residual standard deviation
- sigmaREML
-
REML estimate of residual standard deviation
- tolPwrss
-
tolerance for declaring convergence in the
penalized iteratively weighted residual sum-of-squares (GLMMs only)
The elements of dims are:
- N
-
number of rows of X
- n
-
length of y
- p
-
number of columns of X
- nmp
-
n-p
- nth
-
length of theta
- q
-
number of columns of Z
- nAGQ
-
see glmer
- compDev
-
see glmerControl
- useSc
-
TRUE if model has a scale parameter
- reTrms
-
number of random effects terms
- REML
-
0 indicates the model was fitted by maximum
likelihood, any other positive integer indicates fitting by
restricted maximum likelihood
- GLMM
-
TRUE if a GLMM
- NLMM
-
TRUE if an NLMM
-
"offset":
-
model offset
-
"lower":
-
lower bounds on model parameters (random effects
parameters only).
-
"devfun":
-
deviance function (so far only available for LMMs)
-
"glmer.nb.theta":
-
negative binomial θ parameter,
only for glmer.nb.